title: SU-DIPG-XVII_sgCHD2_H3K27me3_rep2

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the human (hg19) reference genome using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were aligned to hg19 reference using STAR.
Coverage for each base pair of the human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
Sparse Enrichment Analysis for CUT&RUN (SEACR version 1.3) was used for peak calling (Meers et al., 2019). Overlapped peaks between replicates were retained and then merged to obtain a consensus peak set for each Cut&Run target using BEDTools (version 2.29.2) (Quinlan and Hall, 2010).
Read count on gene body or promoters were calculated by FeatureCount. Differential genes and log fold change were calculated by edgeR. The P value of each gene was adjusted using the Benjamini–Hochberg (BH) procedure. Genes with a BH-adjusted P value less than 0.05 and a fold change greater than 1.5 (upregulated) or less than 0.67 (downregulated) were considered as differentially expressed genes (DGEs).
Assembly: hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density.
Library strategy: CUT&RUN

value: Diffuse intrinsic pontine glioma (DIPG) cells

tag: genotype

value: CHD2 KO

tag: chip antibody

tag: spike-in

value: Mus musculus


title: SU-DIPG-XVII_sgCHD2_H3K27me3_rep1

status: Public on May 09 2024

type: SRA

city: New York

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

country: USA

institute: Columbia University

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: patient-derived cell culture

growth_protocol: Patient-derived DMG cells (SU-DIPG-IV, SU-DIPG-VI, SU-DIPG-XVII, SU-DIPG-XXXVI) were obtained from Dr. Michelle Monje at Stanford University and maintained as neurospheres in knockout DMEM/F12 media (Gibco) supplemented with StemPro Neural Supplement (Gibco), 20 ng/ml human FGF-basic (bFGF) (Gibco), 20 ng/ml human EGF (Gibco), 2 mM L-Glutamine (Gioco), 1% penicillin/streptomycin (Invitrogen) and plasmocin (InvivoGen). Alternatively, the DMG cells were maintained as adherent culture using 24 μg/ml fibronectin-coated dishes. Mouse DMG cells with H3.3K27M mutation were obtained from Dr. Oren Becher at Mount Sinai Hospital and maintained as neurospheres in NeuroCult™ Basal Medium (STEMCELL Technologies) containing Neurocult proliferation supplement (STEMCELL Technologies), 20 ng/ml human bFGF (Gibco), 10 ng/ml human EGF (Gibco), 2 μg/mL Heparin (STEMCELL Technologies) and 1% penicillin/streptomycin (Invitrogen). All cells were cultured at 37℃ with 5% CO2, and were periodically tested mycoplasma negative by PCR.

extract_protocol:
CUT&RUN was performed as previously described (Skene and Henikoff, 2017) with minor modifications. Total RNA samples were purified the same as for RT-PCR.
RNA-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. CUT&RUN libraries were prepared using ACCEL-NGSTM 1S plus DNA library kit and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.

tag: cell type


title: PAB_2

city: Shanghai

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

country: China

institute: Shanghai Children's Medical Center

library_source: transcriptomic

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3;WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite).
Assembly: mm10
Supplementary files format and content: FPKM

molecule: total RNA

organism: Mus musculus

source_name: right ventricle

growth_protocol: Mice live with their mother under 19-22℃ with free access to food and water

extract_protocol:
Right ventricular tissue was rapidly removed from executed rat and flash frozen in -80℃ refrigerator, RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Neonatal mouse (within 24h after birth) were subjected to sham and PAB group, mice in PAB group underwent pulmonary artery banding surgery,  mice in sham group underwent same surgical procedures but without banding

tag: strain

tag: tissue

value: right ventricle

value: WT

tag: treatment

value: pulmonary artery banding surgery on postnatal day 1

tag: harvest

value: postnatal day 7


title: Control Subject 30

city: Tel Aviv

first: Avraham

last: Unterman

address: Weizmann 6

country: Israel

institute: Tel Aviv Sourasky Medical Center

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were demultiplexed using Cell Ranger mkfastq pipeline (v3.0.2) to create FASTQ files. Next, Cell Ranger count pipeline (v3.0.2) was employed in order to perform alignment (using STAR), filtering, barcode counting and UMI counting.
Seurat R package (v3.1) was used for all downstream analyses. 10x Genomics gene expression aggregated matrix was converted into a Seurat object using CreateSeuratObject function. Genes expressed by fewer than 3 cells were filtered out. Cells with mitochondrial gene percentages higher than 12% and cells with fewer than 1000 Unique Molecular Identifiers (UMIs) were excluded from the study to filter out dead and dying cells.
Assembly: GRCh38
Supplementary files format and content: For each sample, processed data include Cell Ranger Count filtered outputs: cell barcodes (barcodes.tsv.gz), genes (features.tsv.gz) and count matrix (matrix.mtx.gz).

molecule: polyA RNA

source_name: PBMCs

extract_protocol:
PBMCs were isolated from whole blood by density gradient centrifugation using Histopaque 1077 (Sigma Aldrich) and immediately cryopreserved in 70% DMEM, 20% FBS and 10% DMSO. PBMCs were later thawed and DMSO was removed by 5 serial dilutions in cold growth medium added at 1:1 ratio, followed by cetrifugation and removal of suprenatant. Then, cell pellets were resuspended in PBS + 0.04% BSA, filtered using a 40 micron strainer, counted and loaded to the 10x chromium platform. To minimize batch effects, samples were processed in five randomized and balanced batches of 8, each containing 2-3 samples of each of the 3 patient categories: stable IPF, progressive IPF, and controls. The division into batches can be found in Table E1 in the online manuscript.
Cells from each sample were loaded onto the 10x Chromium Chip A, according to the manufacturer’s user guide (Chromium Single Cell V(D)J Reagent Kits User Guide, document number CG000086, revision J, November 2018), aiming for recovery of 10,000 cells per lane. The loaded Chip A was placed in 10x Chromium Controller to create Gel Beads-in-emulsion (GEMs). The next steps were carried out according to the manufacturer’s user guide, including GEM-RT incubation, post GEM-RT Dynabead cleanup, cDNA amplification and cleanup, fragmentation, end-repair and A-tailing, adaptor ligation, sample Index PCR and double-sided size selection using SPRIselect (Beckman Coulter).

value: PBMCs

tag: group assignment

value: Control

tag: age (years)

tag: Sex

value: Male

tag: race/ethnicity

value: Caucasian

tag: smoking

value: Ever

tag: pack years

tag: dlco% predicted

tag: fvc% predicted


title: Control Subject 27


title: PAB_1


title: Stable IPF patient 26

value: Stable IPF

value: Never


title: Blood, Patient 11

city: White/Caucasian

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

institute: UNMC

data_processing:
Sequencing data was aligned to the human genome using 10X Genomics Cell Ranger before importing into Partek Flow Genomics Suite (RRID: SCR_011860) for the remainder of the analysis.
A standard quality control pipeline was implemented to safeguard against contamination by low-quality cells/reads.
Resulting single-cell count matrices were normalized within Partek Flow using counts per million, add 1, and log base 2 transformed. Samples were then integrated for all downstream analyses.
Assembly: GRCh38-2020-A
Supplementary files format and content: Hierarchical Data Format .h5 files containing count matricies for each sample

source_name: Blood

extract_protocol:
Residual tissues and paired blood samples were collected intraoperatively from patients undergoing craniotomy with debridement for infection treatment after informed consent (IRB #0241-18-EP).  Blood was used as an intrapatient comparator for tissue analysis. Leukocytes were isolated from whole blood using Histopaque, and the resulting plasma layer was collected and frozen for subsequent cytokine/chemokine analysis. The resulting cells were washed with 1X PBS and filtered through a filter-top FACS tube before flow cytometry staining. Tissue samples were homogenized in HBSS with 10% FBS and passed through a 70 μm filter to achieve a single-cell suspension. Samples were centrifuged, supernatant collected for cytokine/chemokine measurements, and cells washed in 1X PBS before RBC lysis. Bone flaps were submerged in 1X PBS and vortexed for 1 min to dislodge adherent cells, which were collected and filtered through a 70 μm filter to remove aggregates. Single cell suspensions were stained for CD45-APC-Cy7 (RRID:AB_312981) and Zombie UV Fixable Viability Kit (BioLegend) and FACS sorted to obtain live CD45+ leukocytes. Samples were evaluated using a Luna automated fluorescent cell counter (Logos Biosystems) to assess cell viability, density, and debris before single-cell capture with a 10X Genomics instrument. Cells were then lysed, and the resulting DNA was reverse-transcribed and barcoded using a Chromium Single Cell 3’ Reagent Kit (v3.1; 10X Genomics) according to the manufacturer's instructions.
Illumina-compatible cDNA libraries were quantified with a Qubit-30 Fluorometer and assessed using a fragment analyzer before loading on a Novaseq6000 instrument at a final concentration of 300pM for generation of 75 bp pair-end reads. Samples sequenced included: patient 7 blood (5215 cells), bone flap (2957 cells), epidural (3459 cells), and intracranial tissue (ICT; 2982 cells); patient 11 blood (3925 cells), bone flap (5583 cells), and subgalea/epidural tissues (4374 cells); patient 14 blood (3645 cells), subgalea (626 cells), and bone flap (2973 cells) tissues; patient 15 blood (16983 cells), epidural (7125 cells), subgalea (4206 cells), and bone flap (7360 cells) tissues. Sequencing was performed to an average depth of 50,000-100,000 reads per cell

value: Blood

tag: cell line

value: Patient 11


title: SU-DIPG-XVII_sgNeg_H3K27me3_rep1

tag: genotype


title: sham_3

value: sham surgery on postnatal day 1


title: SU-DIPG-XVII_sgCHD2_H3K4me3_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells

tag: chip antibody


title: sham_2


title: sh-UHRF1_3

city: Beijing

first: Gong

middle: chun

last: xue

address: 20 East Street, Fengtai District

institute: Beijing Institute of Biotechnology

data_processing:
The library was sequenced on Illumina Novaseq platform. Image analysis and base calling were  performed with Illumina CASAVA pipeline, and finally generated 150bp paired-end reads.
Used FastQC (fastqc_v0.11.5) to perform basic statistics on the quality of the raw reads andpredicted repeats with RepeatMasker, and CGI track from a genome with cpgIslandExt
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated  reads to a reference genome (-X 700 --dovetail) and Methylated sites were identified with a binomial test using the methylated counts (mC), totols counts  (mC+umC) and the non-conversion rate (r). Sites with FDR-corrected p-value<0.05 were considered  as a methylated site.
Differentially methylated regions (DMRs) were identified using the DSS software (Hao Feng, Hao Wu,  2014; Hao Wu, 2015; Yongseok Park Hao Wu,2016) , The core of DSS is a new dispersion shrinkage  method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. According to the distribution of DMRs through the genome, we defined the genes related to DMRs as  genes whose gene body region (from TSS to TES) or promoter region (2 kb upstream from the TSS)  have an overlap with the DMRs.
Gene Ontology (GO) enrichment analysis of genes related to DMRs was implemented by the GOseq  R package (Young MD, 2010), in which gene length bias was corrected. GO terms with corrected P_x0002_value less than 0.05 were considered significantly enriched by DMR-related genes. We used KOBAS  software (Mao X, 2005) to test the statistical enrichment of DMR- related genes in KEGG pathways.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include DMR values for each Sample

source_name: Mammary gland

extract_protocol:
Genomic DNA degradation and contamination was validated by agarose gels. DNA purity was checked  using NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured  using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by  sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using  EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene  Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina  platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Mammary gland

value: Breast cancer cell

value: Lentivirus infection


title: Stable IPF patient 24


title: sh-UHRF1_2


title: SU-DIPG-XVII_sgCHD2_H3K4me3_rep1

value: CHD2 KO


title: sham_1

value: right ventricle

value: WT


title: Stable IPF patient 23

value: PBMCs


title: sh-UHRF1_1


title: SU-DIPG-XVII_sgNeg_H3K4me3_rep2


title: F. columnare challenge hour24 hybrid striped bass rep6 gill tissue

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using  FastQC (v.0.11.8) and Trimmomatic (v.0.38). This was used to trim low-quality ends from reads and for Illumina adapter removal.
All reads were filtered for the removal of 18S, 5.8S, and 28S sequences using the STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) for alignment of sequences to the Morone 18S, 5.8S, and 28S sequences available on GenBank and output of unaligned reads used for subsequent analysis. This was completed as QC indicated the sequence reads WB-1-t4hr and HB-4-t4hr had 52.68% and 68.99% alignment to these sequences, respectively. These individuals were dropped from subsequent analysis.
The STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) were used to align all filtered reads generated for the other 46 samples to the white bass transcriptome using default parameters.
Read-counts were generated using the default parameters of HTSeq (v.0.9.0).
Gene expression fold-changes were determined between groups were determined in a pairwise fashion using edgeR (v.3.28.0) with TMM (Weighted trimmed mean of M-values) as the normalization method, Exact Test, and “robust” filter to strengthen estimations against potential outliers.
Assembly: All RNA transcripts from the white bass transcriptome shotgun assembly GAZY00000000.1 (GAZY01000001-GAZY01183659) in GenBank
Supplementary files format and content: tab-deliminated text file of read counts representing the total number of reads aligned to each genomic feature

organism: Morone chrysops x Morone saxatilis

source_name: gill

growth_protocol: Fingerling white bass (WB) and hybrid striped bass (HB) (N=480 total, 240 of each) randomly selected from populations spawned indoors and reared in ponds to 2-3 months of age at the Harry K Dupree Stuttgart National Aquaculture Research Center (Stuttgart, Arkansas, USA) and stocked into 16 total replicate 18 L tanks (8 tanks for WB and 8 for HB, n=30 fish per tank). Fish were fed to apparent satiation 3 days per week, for 2 weeks prior to the study. Fish were not fed on the day before bacterial challenge or thereafter.

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Total RNA was standardized to 100 ng each sample. Sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Barcodes used were the NEBNext Multiplex Oligos for Illumina (Index Primers Sets 1 and 2).

treatment_protocol: White bass (WB) and hybrid striped bass (HB) in the control group (t0hr) were given a mock treatment and sampled immediately prior to aquaria being challenged with 10 mL culture of Flavobacterium columnare isolate LSU-066-04 (0.70 absorbance at 550nm; 6.3X10^6 CFU/mL). Water was provided through the ultra-low-flow water delivery system at a rate of 30 ml/min for 24h then flow was increased to 200 mL/min. Fish were observed twice daily for the recording and removal of any dead or moribund fish, and fish were formally sampled at three timepoints after the challenge had been initiated, 1 hour post treatment (t1hr), 4 hours post treatment (t4hr), and 24 hours post treatment (t24hr).

tag: animal

value: hybrid striped bass (HB)

value: gill

value: Flavobacterium columnare immersion

tag: time

value: 24 hr after immersion


title: Stable IPF patient 22

tag: cell type

value: Stable IPF

value: Female

value: Caucasian


title: Bone Flap, Patient 11

source_name: Bone Flap

tag: tissue

value: Bone Flap

value: Patient 11


title: sh-Scramble_3

value: sh-Scramble

tag: treatment


title: SU-DIPG-XVII_sgNeg_H3K27me3_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells

tag: spike-in

value: Mus musculus


title: SU-DIPG-XVII_sgNeg_H3K4me3_rep1


title: F. columnare challenge hour4 hybrid striped bass rep6 gill tissue

value: 4 hr after immersion


title: sh-Scramble_2

value: Mammary gland

value: Breast cancer cell

value: Lentivirus infection


title: F. columnare challenge hour1 hybrid striped bass rep6 gill tissue

value: 1 hr after immersion


title: Stable IPF patient 20

value: PBMCs

tag: group assignment

value: Ever


title: sh-Scramble_1


title: Stable IPF patient 21

tag: age (years)

value: Male


title: SU-DIPG-IV_sgFOSL1_H3K27me3_rep2

value: FOSL1 KO


title: F. columnare challenge hour0 hybrid striped bass rep6 gill tissue

value: hybrid striped bass (HB)

value: gill

value: control mock immersion

value: 0 hr after mock treatment


title: SU-DIPG-IV_sgFOSL1_H3K27me3_rep1


title: Stable IPF patient 25

value: Stable IPF

tag: Sex

value: Caucasian


title: F. columnare challenge hour24 hybrid striped bass rep5 gill tissue

value: Flavobacterium columnare immersion

value: 24 hr after immersion


title: UHRF1-shRNA_3

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence\low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GRCh37 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity
Read count extration and nomalization were performed using CLC genomic benchwork
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include RPKM values and DEG values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols


title: Stable IPF patient 19

tag: race/ethnicity


title: SU-DIPG-IV_WT_H3K27me3_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: WT

value: Mus musculus


title: Stable IPF patient 18

tag: smoking


title: SU-DIPG-IV_WT_H3K27me3_rep1


title: UHRF1-shRNA_1

value: Mammary gland

value: Breast cancer cell

value: Lentivirus infection


title: UHRF1-shRNA_2


title: F. columnare challenge hour1 hybrid striped bass rep5 gill tissue

value: 1 hr after immersion


title: Stable IPF patient 17

value: PBMCs

value: Male

value: Ever

tag: pack years


title: F. columnare challenge hour4 hybrid striped bass rep5 gill tissue

value: hybrid striped bass (HB)

value: gill

value: 4 hr after immersion


title: SU-DIPG-IV_sgFOSL1_H3K27Ac_rep2

value: FOSL1 KO


title: Scramble-shRNA _3

value: sh-Scramble


title: SU-DIPG-IV_sgFOSL1_H3K27Ac_rep1


title: Stable IPF patient 16

value: Stable IPF

value: Caucasian

tag: dlco% predicted


title: F. columnare challenge hour0 hybrid striped bass rep5 gill tissue

value: control mock immersion

value: 0 hr after mock treatment


title: Stable IPF patient 15

value: Never

tag: fvc% predicted


title: Scramble-shRNA _2

value: Mammary gland

tag: cell line


title: F. columnare challenge hour24 hybrid striped bass rep4 gill tissue

value: Flavobacterium columnare immersion

value: 24 hr after immersion


title: Scramble-shRNA _1

value: Breast cancer cell

tag: genotype

value: Lentivirus infection


title: SU-DIPG-IV_WT_H3K27Ac_rep1

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: WT

tag: chip antibody

value: Mus musculus


title: F. columnare challenge hour4 hybrid striped bass rep4 gill tissue

tag: animal

value: hybrid striped bass (HB)

value: gill


title: SU-DIPG-IV_WT_H3K27Ac_rep2


title: Stable IPF patient 14

value: PBMCs

value: Female

value: Ever


title: W043F_D6_post_suG

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Samples were analyzed using the nf-core rnaseq pipeline version 3.10.1 [https://nf-co.re/rnaseq/1.4.2] with nextflow version v22.10.4.
The intial fastq reads of all the samples were processed by Trimmgalore to trim/filter Illumina adapter sequences if any before processing further.
Reads aligned by STAR and gene expression values of each sample generated by Salmon program.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Human umbilical cord

growth_protocol: hWJSCs were maintained in DMEM high glucose supplemented with 20% fetal bovine serum (FBS), 1% non-essential amino acids, 2 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1% insulin-transferrin-selenium (ITS), antibiotic-antimycotic mixture and 16 ng/ml basic fibroblast growth factor (bFGF), in humidified atmosphere with  5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy Mini Kit (Qiagen). 1000ng of total RNA (minimum RIN value 9.0) in a 25μl volume was submitted for sequencing.
RNA-seq library preparation (3’ directional, polyA enrichment) and bulk RNA sequencing (NovaSeq PE150) was performed on total RNA by Novogene (Singapore). Samples were sequenced to a target depth of 30 million reads.

treatment_protocol: hWJSCs were exposed to stimulated lunar microgravity (0.16G) for 3 days using a Random Postioning Machine, and then exposed to terrestrial gravity (1.0G) for another 3 days.  Separate control lines accounting for alterations in cell culture gas exchange and sμG were ran in parallel.

value: Human umbilical cord

value: Human Wharton's Jelly Stem Cells

value: Mesenchymal Stem Cells

value: F

tag: time

value: Stimulated microgravity


title: Progressive IPF patient 12

tag: cell type

value: Progressive IPF

value: Male

value: Asian Indian

value: Never


title: Progressive IPF patient 11

value: Caucasian


title: F. columnare challenge hour1 hybrid striped bass rep4 gill tissue

tag: tissue

value: Flavobacterium columnare immersion

value: 1 hr after immersion


title: F. columnare challenge hour0 hybrid striped bass rep4 gill tissue

value: hybrid striped bass (HB)

tag: treatment

value: control mock immersion

value: 0 hr after mock treatment


title: SU-DIPG-IV_sgFOSL1_H3K4me3_rep1

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: FOSL1 KO


title: Progressive IPF patient 10

value: PBMCs

value: Ever


title: W040F_D6_post_suG

value: Human umbilical cord

value: Human Wharton's Jelly Stem Cells

value: Mesenchymal Stem Cells


title: W042M_D6_post_suG

value: M

value: Stimulated microgravity


title: F. columnare challenge hour24 hybrid striped bass rep3 gill tissue

value: gill

value: 24 hr after immersion


title: Progressive IPF patient 9

value: Progressive IPF

value: Male

value: Caucasian

value: Never


title: W037M_D6_post_suG


title: SU-DIPG-IV_sgFOSL1_H3K4me3_rep2


title: SU-DIPG-IV_WT_H3K4me3_rep1

value: WT


title: F. columnare challenge hour4 hybrid striped bass rep3 gill tissue

value: hybrid striped bass (HB)

value: Flavobacterium columnare immersion

value: 4 hr after immersion


title: W033F_D6_post_suG

value: F


title: Progressive IPF patient 8

value: PBMCs

value: Ever


title: SU-DIPG-IV_sgCHD2_H3K27me3_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: CHD2 KO

tag: spike-in

value: Mus musculus


title: F. columnare challenge hour1 hybrid striped bass rep3 gill tissue

value: 1 hr after immersion


title: Progressive IPF patient 7

tag: group assignment

value: Female


title: SU-DIPG-IV_sgCHD2_H3K27me3_rep1


title: W005M_D6_post_suG

value: Human umbilical cord

value: Human Wharton's Jelly Stem Cells

value: Mesenchymal Stem Cells

value: M

value: Stimulated microgravity


title: F. columnare challenge hour0 hybrid striped bass rep3 gill tissue

value: gill

value: control mock immersion

value: 0 hr after mock treatment


title: Progressive IPF patient 6

value: Progressive IPF

tag: age (years)

value: Male

value: Caucasian


title: W042M_D3_suG

tag: Sex


title: SU-DIPG-IV_sgNeg_H3K27me3_rep2

value: WT


title: F. columnare challenge hour24 hybrid striped bass rep2 gill tissue

value: hybrid striped bass (HB)

value: Flavobacterium columnare immersion

value: 24 hr after immersion


title: Progressive IPF patient 5

value: PBMCs

tag: race/ethnicity

value: Ever


title: W040F_D3_suG

value: Human umbilical cord

value: F


title: SU-DIPG-IV_sgNeg_H3K27me3_rep1

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: Mus musculus


title: F. columnare challenge hour4 hybrid striped bass rep2 gill tissue

value: 4 hr after immersion


title: SU-DIPG-IV_WT_H3K4me3_rep2


title: Progressive IPF patient 4

tag: smoking

value: Never


title: SU-DIPG-IV_sgCHD2_H3K27Ac_rep2

value: CHD2 KO


title: F. columnare challenge hour1 hybrid striped bass rep2 gill tissue

value: gill

value: 1 hr after immersion


title: Progressive IPF patient 3

value: Progressive IPF

value: Male

tag: pack years


title: W033F_D3_suG

value: Human Wharton's Jelly Stem Cells

value: Mesenchymal Stem Cells

value: Stimulated microgravity


title: SU-DIPG-IV_sgCHD2_H3K27Ac_rep1


title: W013F_D3_suG


title: Progressive IPF patient 2

value: Caucasian

tag: dlco% predicted


title: F. columnare challenge hour0 hybrid striped bass rep2 gill tissue

value: hybrid striped bass (HB)

value: control mock immersion

value: 0 hr after mock treatment


title: SU-DIPG-IV_sgNeg_H3K27Ac_rep2

value: WT


title: Progressive IPF patient 1

value: PBMCs

tag: fvc% predicted


title: F. columnare challenge hour24 hybrid striped bass rep1 gill tissue

value: Flavobacterium columnare immersion

value: 24 hr after immersion


title: SU-DIPG-IV_sgNeg_H3K27Ac_rep1

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: Mus musculus


title: F. columnare challenge hour4 hybrid striped bass rep1 gill tissue

value: gill

value: 4 hr after immersion


title: Muller glia from mycb-/- retinas 2 days post injury (dpi) rep2 [7131-ML-8] [7131-ML-8]

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.3.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCz11
Supplementary files format and content: RS11_deseq2_raw_counts.txt
Supplementary files format and content: tab-delimited text with include expected counts values for each Sample

organism: Danio rerio

source_name: mycb-/- Muller glia injured retina

extract_protocol:
Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes, tissue was dissociated using Papain Dissociation system (Worthington Biochemical) and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit (Zymo Research).
Illumina RNA (PolyA-enrichment) library prep kit was used according to manufacturer's directions.

treatment_protocol: Needle poke injury to retina.

value: mycb-/- Muller glia injured retina

value: mycb-/-

value: injured


title: W005M_D3_suG

value: Human umbilical cord

tag: cell line

value: Human Wharton's Jelly Stem Cells

value: Mesenchymal Stem Cells

value: M


title: F. columnare challenge hour1 hybrid striped bass rep1 gill tissue

value: hybrid striped bass (HB)

value: 1 hr after immersion


title: SU-DIPG-IV_sgCHD2_H3K4me3_rep2

tag: genotype

value: CHD2 KO


title: Muller glia from mycb-/- retinas 2 days post injury (dpi) rep1 [7131-ML-7] [7131-ML-7]


title: F. columnare challenge hour0 hybrid striped bass rep1 gill tissue

value: control mock immersion

value: 0 hr after mock treatment


title: SU-DIPG-IV_sgCHD2_H3K4me3_rep1

tag: chip antibody


title: W042M_D6_ExptCtrl

value: Stimulated microgravity


title: Muller glia from WT retinas 2 days post injury (dpi) rep2 [7131-ML-5] [7131-ML-5]

source_name: WT Muller glia injured retina

value: WT Muller glia injured retina

value: WT


title: SU-DIPG-IV_sgNeg_H3K4me3_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells


title: W037M_D3_suG


title: Control female rep 3

city: Balitmore

first: Mark

last: Van Doren

state: Maryland

address: 3400 N Charles street, Mudd Hall

department: Biology

institute: Johns Hopkins University

data_processing:
Quality of raw reads was assessed using the fastQC kit (Babraham Institute).
RNA-Seq reads were mapped to the Drosophila genome using Ensembl BDGP6 release 85,  TopHat 2.1.1, and HTSeq 0.9.1
Differential gene expression analysis was done using DESeq using ensemble annotation BDGP6
Assembly: dmel 6
Supplementary files format and content: htseq output files of gene counts

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
Gonads were dissected from 1-2 day old male flies or 0-1day old female flies raised at 25°C. 3 biological replicates were dissected for each genotype. RNA from males was prepped using ribodepletion. RNA from females was prepped using The Direct-zol RNA micro prep 481 kit (Zymogen).
200ng of RNA was used to prepare each library using the illumina TruSeq RNA Library Prep kit v2

value: ovary

value: cas9 iso

value: female

tag: fraction

value: Poly A selected RNA


title: Muller glia from WT retinas 2 days post injury (dpi) rep1 [7131-ML-4] [7131-ML-4]


title: W042M_D3_ExptCtrl

value: Human umbilical cord

tag: time


title: SU-DIPG-IV_sgNeg_H3K4me3_rep1

tag: cell type


title: Muller glia from uninjured WT retinas rep2 [7131-ML-2] [7131-ML-2]

source_name: WT Muller retinal glia

tag: tissue

value: WT Muller retinal glia


title: Control female rep 2


title: W040F_D6_ExptCtrl

value: Human Wharton's Jelly Stem Cells

value: Mesenchymal Stem Cells

value: F

tag: treatment


title: SU-DIPG-IV_sgFOSL1_FOSL1_rep2

value: FOSL1 KO


title: Muller glia from uninjured WT retinas rep1 [7131-ML-1] [7131-ML-1]


title: W012M_D3_suG

value: M


title: Control female rep 1


title: Tdrd5l mutant female rep 3

value: Tdrd5l mutant


title: W040F_D3_ExptCtrl


title: SU-DIPG-IV_sgFOSL1_FOSL1_rep1


title: Muller glia from mych-/- retinas 2 days post injury (dpi) rep3 [5803-ML-10]

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.3.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCz11
Supplementary files format and content: RS10_deseq2_raw_counts.txt
Supplementary files format and content: tab-delimited text with include expected counts values for each Sample

source_name: mych-/- Muller glia injured retina

value: mych-/- Muller glia injured retina

value: mych-/-

value: injured


title: W037M_D6_ExptCtrl

value: Stimulated microgravity


title: SU-DIPG-IV_FOSL1_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: WT


title: Tdrd5l mutant female rep 2

value: ovary


title: W043F_D6_ExptCtrl


title: W037M_D3_ExptCtrl


title: Muller glia from mych-/- retinas 2 days post injury (dpi) rep2 [5803-ML-8]


title: SU-DIPG-IV_FOSL1_rep1


title: Tdrd5l mutant female rep 1

value: female


title: Muller glia from mych-/- retinas 2 days post injury (dpi) rep1 [5803-ML-7]


title: W033F_D6_ExptCtrl


title: SU-DIPG-IV_sgFOSL1_CHD2_rep2


title: Muller glia from WT retinas 2 days post injury (dpi) rep3 [5803-ML-6]

value: WT Muller glia injured retina


title: W013F_D3_ExptCtrl

value: Human umbilical cord


title: Control male rep 2

source_name: testis

value: testis

value: cas9 iso

value: male

value: Ribo depleted RNA


title: Muller glia from WT retinas 2 days post injury (dpi) rep2 [5803-ML-5]


title: SU-DIPG-IV_sgFOSL1_CHD2_rep1

value: FOSL1 KO


title: Control male rep 3


title: SU-DIPG-XVII_CHD2_rep2


title: Muller glia from WT retinas 2 days post injury (dpi) rep1 [5803-ML-4]


title: Muller glia from uninjured WT retinas rep3 [5803-ML-3]

source_name: WT Muller glia uninjured retina

value: WT Muller glia uninjured retina


title: W033F_D3_ExptCtrl

value: Human Wharton's Jelly Stem Cells

value: Mesenchymal Stem Cells

value: F


title: Tdrd5l mutant male rep 3

value: Tdrd5l mutant


title: W005M_D6_ExptCtrl

value: M

value: Stimulated microgravity


title: SU-DIPG-IV_CHD2_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: WT


title: Tdrd5l mutant male rep 2


title: W005M_D3_ExptCtrl


title: SU-DIPG-XVII_CHD2_rep1


title: Muller glia from uninjured WT retinas rep2 [5803-ML-2]


title: Tdrd5l mutant male rep 1


title: W012M_D3_ExptCtrl


title: Muller glia from uninjured WT retinas rep1 [5803-ML-1 ]


title: Newborn lens epithelium miRNAs_3

status: Public on May 08 2024

city: OXFORD

first: Anil

last: Upreti

state: OH

address: 501 E High St, Oxford, OH 45056

institute: Miami University

data_processing:
Raw reads were quality-analyzed using FastQC and MultiQC .
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cut adapt and trim galore with paramaters  -q 20 --phred33 --length 20.
Trimmed sequence reads were mapped to GrCM39 using Hisat2 incorporating splice juncation from genecode GTF .
Gene counts were generated using Stringtie2.1.5. For microRNA-sequencing, bowtie (version1.3.1) was used for alignment followed by mirdeep2 (0.1.2) and the miRbase release 22.1
Differential expression testing was performed with DESeq2.
Assembly: GRCm39 v.M27
Supplementary files format and content: Normalized gene count matrix from DESeq2 mRNAs. Count file for miRNA.

source_name: Lens Epithelium

extract_protocol:
For miRNA-sequencing: Total RNA was extracted using mirVanaTM miRNA isolation kit (# AM1560, ThermoFisher Scientific). Small RNA was isolated from total RNA by size-selection and NEBNext Multiplex Small RNA Library Prep Kit was used for 50bp-single-ended sequencing. For mRNA sequencing Total RNA was extracted using the RNEasy Mini Kit (Qiagen cat. 74104) following the manufacturer’s instructions.
For miRNA libraries were prepared in Genomics and Sequencing core, University of Cincinnati using NEBNext Multiplex Small RNA Library Prep Kit. For mRNA sequencing RNA libraries were constructed by Novogene (Sacramento, CA, USA) using a TruSeq (Illumina) library prep kit.

value: Lens Epithelium

value: FVB/N


title: Newborn lens fiber cell miRNAs_3

source_name: Lens Fiber cells

value: Lens Fiber cells


title: Newborn lens fiber cell miRNAs_2


title: Newborn lens epithelium miRNAs_2


title: Newborn lens fiber cell miRNAs_1


title: Newborn lens epithelium miRNAs_1


title: PKM2ΔMAC, MCD8w, scRNA-seq

city: Guangzhou

first: Liu

last: Junli

state: Guangdong

address: Guangzhou, Jinan university

institute: jinan university

description: 10X Genomics

data_processing:
Data was mapped using Cell Ranger (10X Genomics) to mm10.
Single-cell RNA seq data was processed by Seurat package (v.4.3.0)
The cells with low quality and high mitochondrial content were removed.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: Liver

extract_protocol:
Nonparenchymal cells were isolated by liver perfusion and density gradient centrifugation
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq , depends on project) according to the manufacturer’s instructions (Illumina)

treatment_protocol: Liver non-parenchymal cells from PKM2ΔMAC and PKM2FL/FL mice fed with MCD diet for 8 weeks were subjected to scRNA-seq

value: Liver

value: Liver non-parenchymal cells

value: Fed with MCD diet for 8 weeks


title: Control male rep 1

value: testis

value: cas9 iso

value: male

value: Ribo depleted RNA


title: PKM2FL/FL, MCD8w, scRNA-seq

description: 10X Genomics


title: 43_MEKi.SPP1.CD44_2

city: Zurich

first: Lukas

last: Sommer

state: Zurich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

description: 150 bp

data_processing:
FASTQ files were checked for quality with FastQC (version 0.11.9) and trimmed using Trimmomatic (version 0.39). Trimmed fastq files were aligned to the human genome annotation (retrieved from Ensembl) using STAR algorithm (version 2.7.10a)
Assembly: GRCh38 release 105
Supplementary files format and content: tab delimited text file including raw counts for each sample

extract_protocol:
RNA was collected using the Direct-zol RNA MiniPrep according to manufacturer’s guidelines. The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent, Santa Clara, California, USA). The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.
Illumina TruSeq mRNA stranded

treatment_protocol: M150543 melanoma cells were treated with MEKi  for 20 hours alone or in combinatorial treatments: SPP1+MEKi; CD44 blocking antibody +MEKi; or SPP1+CD44 blocking antibody+MEKi. The pre-stimulations with SPP1 or CD44 blocking antibody was performed 2 hours before MEKi treatment.

value: melanoma


title: 43_MEKi.SPP1.CD44_1

description: 150 bp


title: 43_MEKi.SPP1_1

description: 150 bp


title: SU-DIPG-IV_CHD2_rep1

source_name: patient-derived cell culture


title: melanoma_frozen_23 [20200204_Karen2_01_11]

type: RNA

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

hyb_protocol: 200 ng RNA was hybridized to a custom NanoString panel code set according to the recommendations of the manufacturer (NanoString Technologies, Inc., Seattle, Washington, USA).

scan_protocol: Following hybridization, the target-probe complexes were purified and immobilized on the nCounter prep station. Digital counts for each gene-specific target RNA were then acquired on the nCounter detection analyzer and normalized to account for differences in tissue mRNA quantity as well as slight differences in assay efficiency.

data_processing: The nSolver analysis software version 4.0 (NanoString Technologies) was used for extraction of raw digital counts of expression, checking the quality of the data, normalizing expression values using housekeeping genes, and generating heatmaps.

label: customized panel

source_name: primary melanoma frozen tissue

label_protocol: Specimens were labeled with decode assignment which was linked to tumor origin.

growth_protocol: This cohort includes human tissue obtained from FFPE (n=205), fresh frozen human tissue (n=24), and human cell lines (n=12).

extract_protocol: RNA was obtained from the FFPE human tissue samples using the RecoverAll Total Nucleic Acid Isolation kit. RNA was obtained from the fresh frozen human tissue samples using the Qiagen Rneasy kit. Cell lines were pelleted and RNA was harvested using the Qiagen Rneasy kit.

tag: gender

tag: age at diagnosis

tag: cohort

value: Mount Sinai

tag: tnm

tag: stage at original diagnosis

tag: ajcc thickness

tag: breslow thickness

tag: ulceration

tag: os

tag: pfs

tag: dead or alive at last contact

tag: tag

value: primary cutaneous melanoma tissue


title: melanoma_frozen_24 [20200204_Karen2_01_12]

value: F


title: melanoma_frozen_21 [20200204_Karen2_01_09]

value: Ia

value: Absent

value: Alive


title: melanoma_frozen_22 [20200204_Karen2_01_10]

value: M


title: 43_MEKi.SPP1_2

description: 150 bp

tag: cell line


title: melanoma_frozen_20 [20200204_Karen2_01_08]


title: 43_MEKi_1

description: 150 bp

value: MEKi


title: melanoma_frozen_18 [20200204_Karen2_01_06]

value: IIa

value: Present


title: melanoma_frozen_19 [20200204_Karen2_01_07]


title: 43_MEKi_2

description: 150 bp


title: 43_MEKi.CD44_3

description: 150 bp


title: melanoma_frozen_17 [20200204_Karen2_01_05]


title: 43_MEKi.CD44_1

description: 150 bp


title: melanoma_frozen_15 [20200204_Karen2_01_03]

value: Ib


title: 43_MEKi.CD44_2

description: 150 bp


title: melanoma_frozen_13 [20200204_Karen2_01_01]


title: melanoma_frozen_14 [20200204_Karen2_01_02]

value: IIb


title: melanoma_frozen_11 [20200204_Karen1_01_11]

value: IIc

value: Dead


title: LSS2

city: Higashi-hiroshima

first: Anisa

middle: Nazera

last: Fauzia

state: Hiroshima

address: 1-4-4 Kagamiyama

department: Graduate School of Integrated Sciences for Life

country: Japan

institute: Hiroshima University

data_processing:
This project uses the filtering software SOAPnuke
RNA-seq reads were mapped using HISAT software
Assembly: mm10
Supplementary files format and content: excel file includes log2fc for each sample

organism: Oryza sativa

source_name: leaf sheath

growth_protocol: plant samples grow hydropically

extract_protocol:
Total RNA from the leaves was extracted using Sepasol-RNA I Super G (Nacalai Tesque Inc., Kyoto, Japan), followed by an RNA extraction Kit Mini (Real Genomic RBC Bioscience, Taiwan) with DNase I digestion
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following the manufacturer's protocol

treatment_protocol: salt stress treatment using NaCl 100 mM for 24 h

value: leaf sheath

value: salt stress


title: melanoma_frozen_12 [20200204_Karen1_01_12]


title: LSS1


title: LSC2

value: control


title: 43_MEKi_3

description: 150 bp

value: melanoma


title: melanoma_frozen_8 [20200204_Karen1_01_08]

value: Mount Sinai

value: IIIb

value: primary cutaneous melanoma tissue


title: melanoma_frozen_9 [20200204_Karen1_01_09]

value: Absent


title: LSC1


title: LBS1

source_name: leaf blade

value: leaf blade


title: LBS2


title: melanoma_frozen_16 [20200204_Karen2_01_04]

value: M

value: Alive


title: LBC1


title: melanoma_frozen_5 [20200204_Karen1_01_05]

value: IIIc


title: melanoma_frozen_7 [20200204_Karen1_01_07]

value: F

value: Present


title: melanoma_frozen_6 [20200204_Karen1_01_06]


title: Crosslinked HEK293T, FUS IP, Replicate 1

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: FUS

data_processing:
Read1 data was processed using Skipper, available at: https://github.com/yeolab/skipper
Reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using skewer.
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with fastp
Extracted reads were aligned using STAR: --alignEndsType EndToEnd --genomeDir {params.star_sjdb} --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix {params.outprefix} --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterScoreMin 10 --outFilterType BySJout --limitOutSJcollapsed 5000000 --outReadsUnmapped None --outSAMattrRGline ID:{wildcards.replicate_label} --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --readFilesCommand zcat --outStd Log --readFilesIn {input.fq} --runMode alignReads --runThreadN {threads}
Custom scripts called reproducible enriched windows and repetitive elements as part of Skipper
Assembly: GRCh38
Supplementary files format and content: reproducible enriched window files contain p values, q values, enrichment, and annotations for significantly bound transcriptome tiled windows
Supplementary files format and content: reproducible enriched re files contain p values, q values, enrichment, and annotations for significantly bound repetitive elements

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and complexes were immunoprecipitated with protein-specific antibodies from Bethyl Laboratories
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)

tag: genotype

value: antibody:Anti-FUS, A300-294A lot#1


title: melanoma_frozen_4 [20200204_Karen1_01_04]

value: IIc


title: Crosslinked HEK293T, FUS IN, Replicate 2

description: size-matched input


title: melanoma_frozen_2 [20200204_Karen1_01_02]

value: IIa

value: Dead


title: melanoma_frozen_1 [20200204_Karen1_01_01]

value: IIIa


title: melanoma_frozen_3 [20200204_Karen1_01_03]


title: melanoma_frozen_10 [20200204_Karen1_01_10]

value: IIb


title: melanoma_FFPE_203 [20191220_Karen5_01_09]

source_name: primary melanoma FFPE tissue

value: Zurich

value: IIA


title: melanoma_FFPE_202 [20191220_Karen5_01_08]

value: IIIC


title: MCF10A, TAp63β overexpression, p63 enhancer library, RNA

city: Albany

first: Morgan

middle: A

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

description: PCR amplified cDNA (STARR-seq transcript)

data_processing:
Raw reads were counted by searching for exact match in the designed enhancer library pool sequences in the fastq file using a custom python script.
Assembly: Assembly: GRCh38
Supplementary files format and content: Comma-delimited, raw read counts for each enhancer variant sequence in plasmid DNA pool and STARRSeq RNA from each condition.

source_name: MCF10A TAp63beta dox-induced overexpression

growth_protocol: All human mammary epithelial cell lines MCF-10A TP53+/+ and TP53-/- (Sigma-Millipre clls1049) were cultured in 1:1 Dulbecco’s Modified Eagle’s Medium: Ham’s F-12 (Gibco, #11330-032), supplemented with 5% Horse Serum, (Gibco, #16050-122), 20 ng/mL epidermal growth factor (Peprotech, #AF-100-15), 0.5 µg/mL hydrocortisone (Sigma, #H-0888), 100 ng/mL cholera toxin (Sigma, #C-8052), 10 µg/mL insulin (Sigma, #I-1882), and 1% penicillin-streptomycin (Gibco, #15240-062).A total of approximately 50 million cells were used for each experimental relicate.

extract_protocol:
Total RNA was extracted (Quick RNA, Zymo, #R1055). 30 µg per sample of poly-adenylated mRNA was isolated using oligo d(T) beads (NEB E7490L).
Resulting mRNA was split into 6 separate reactions and cDNA was synthesized using a gene-specific primer (SL1972) and MultiScribe Reverse Transcriptase (Invitrogen, 4311235) . Following cDNA synthesis, all cDNA samples were pooled and one junction-PCR reaction was performed with 16 cycles (SL1973, SL1974) and I5 and i7 primers from NEBNext Oligo Kit (E7600S) were used for Illumina barcoding with between 5 and 9 cycles. MPRA plasmid DNA pools were amplified with i5 and i7 primers as a control for oligo representation. All libraries were pooled and sequenced as single-end, 100bp on an Illumina NextSeq 2000 instrument at the University at Albany Center for Functional Genomics.
STARR-Seq

treatment_protocol: 10 µg of plasmid library were transfected per 5 mln cells via lipofection (Polyplus #101000046, #101000025).  For MCF10A TAp63β inducible cell line and negative control (Gus) cell line, doxycycline was added at 500 ng/ml at the same time as transfection. Cells were harvested after 24h.

value: TAp63beta dox-induced overexpression

value: 500 ng/ml Doxycycline


title: MCF10A, GUS overexpression, p63 enhancer library, RNA

source_name: MCF10A Gus dox-induced overexpression

value: MCF10A Gus dox-induced overexpression

value: Gus dox-induced overexpression


title: SCC25, p63 enhancer library, replicate 2, RNA

value: WT


title: SCC25, p63 enhancer library, replicate 1, RNA


title: HaCaT, p63 enhancer library, replicate 2, RNA

source_name: HaCaT

value: HaCaT


title: LBC2

value: leaf blade

value: control


title: melanoma_FFPE_201 [20191220_Karen5_01_06]

value: F

value: Absent

value: Alive

value: primary cutaneous melanoma tissue


title: Crosslinked HEK293T, FUS IP, Replicate 2

description: FUS

value: antibody:Anti-FUS, A300-294A lot#1


title: melanoma_FFPE_200 [20191220_Karen5_01_05]

value: M

value: IV

value: Present

value: Dead


title: melanoma_FFPE_198 [20191220_Karen5_01_03]

value: Zurich


title: melanoma_FFPE_199 [20191220_Karen5_01_04]


title: MCF10A p53KO, p63 enhancer library, replicate 1, RNA

source_name: MCF10A p53KO

value: MCF10A p53KO


title: MCF10A p53KO, p63 enhancer library, replicate 2, RNA


title: Crosslinked HEK293T, FUS IN, Replicate 1

description: size-matched input


title: MCF10A, p63 enhancer library, replicate 2, RNA


title: K562, Y391K-LSD1GFP_antiIgG-rep2,CUT&RUN

city: Boston

first: Kwangwoon

last: Lee

state: MA

address: 77 Avenue Louis Pasteur, NRB 164

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
CUT&RUN data processing was mostly adopted from the established protocol (Zheng Y et al (2020). Protocol.io, CUT&Tag Data Processing and Analysis Tutorial). FastQ data files were initially processed by fastp (v. 0.23.4), and quality checks were assessed by FastQC (v. 0.11.9). The paired-end reads were aligned to the human reference genome (GRCh38 assembly) using Bowtie2 (v. 2.4.4) as well as the E. coli genome (K-12 MG1655).
For GRch38 assembly, the following arguments were used: bowtie2 -p 8 --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -x /path-to-genome/ /GRCh38_noalt_as. For E. coli, the following arguments were used: bowtie2 -p 8 --end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700 -x /path/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/genome.
The sam output files were converted to the bam format using Samtools (v. 1.17).
For peakcalling, bam files were first converted to bed and bedgraph files using Bedtools (v. 2.31.0) and SEACR relaxed mode85 was used to call peaks by normalizing against the IgG control bedgraph files for each replicate. For CUT&RUN signal visualization, bam files were sorted by the coordinates and indexed using Samtools (v. 1.17), and the sorted bam files were converted to the bigwig files using bamCoverage application from the Deeptools package (v. 3.5.2).
RPGC normalization mode using the effective Genome size of 3049315783 bp and bin size of 1 was applied (bamCoverage -b "$file" -p 10 --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 3049315783 --extendReads --outFileFormat bigwig). The bigwig files were visualized by using Integrative Genomics Viewer (IGV) and analyzed using computeMatrix and plotProfile applications from the Deeptools package (v. 3.5.2).
Assembly: hg38
Supplementary files format and content: bigWig, peak files (except for IgG control)
Library strategy: CUT&RUN

growth_protocol: RPMI1640, 10% fetal bovine serum, 2 mM L-glutamine, 1x penicillin/streptomycin. Cells were cultured at 37 degrees C and 8% CO2

extract_protocol:
Protocol was adapted from Epicypher's CUTANA CUT&RUN Protocol (https://www.epicypher.com/resources/protocols/cutana-cut-and-run-protocol/). Briefly, K562 cells were harvested through centrifugation, bound to ConA beads, permeabilized with digitonin, incubated with antibodies, washed, incubated with pAG-Mnase in the presence of CaCl2, and quenched with EDTA/EGTA along with 0.5 ng of E. coli spike-in DNA to extract DNA.
CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, #E7645S) complemented with NEBNext Multiplex Oligos for Illumina Index Primers Set 1 to 4 (New England Biolabs). 0.5 ng to 11 ng of DNA was used as starting material for all the samples. Libraries were amplified using 14 cycles on the thermalcycler. Post amplification libraries were selected at 250-700 bp in length using AMPure XP beads (Beckman Coulter, #A63880). Libraries were validated using Tapestation (Agilent D1000).

treatment_protocol: Parental K562 cells are homozygously edited with LSD1-GFP. Edited K562 cells are heterozygously edited with Y391K-LSD1-GFP (2 alleles with Y391K-LSD1-GFP and 1 allele with wt-LSD1-GFP)

tag: cell type

value: human immportalized chronic myelogenous leukemia

tag: cut&run antibody

value: Millipore Sigma, #I5006


title: melanoma_FFPE_205 [20191220_Karen5_01_11]


title: MCF10A, p63 enhancer library, replicate 1, RNA

value: WT

tag: treatment


title: melanoma_FFPE_197 [20191220_Karen5_01_02]

tag: gender


title: K562, wtLSD1GFP_antiIgG-rep2,CUT&RUN

value: parental wtLSD1-GFP


title: melanoma_FFPE_204 [20191220_Karen5_01_10]

tag: age at diagnosis

value: IIIC


title: melanoma_FFPE_195 [20191219_Karen4_01_12]

tag: cohort


title: melanoma_FFPE_193 [20191219_Karen4_01_10]

value: Columbia

value: IIB


title: melanoma_FFPE_194 [20191219_Karen4_01_11]

tag: tnm


title: melanoma_FFPE_192 [20191219_Karen4_01_09]

tag: stage at original diagnosis


title: melanoma_FFPE_196 [20191220_Karen5_01_01]

tag: ajcc thickness

value: Absent


title: K562, wtLSD1GFP_antiIgG-rep1,CUT&RUN


title: K562, Y391K-LSD1GFP_antiH3K14ac-rep2,CUT&RUN

value: Millipore Sigma, #07-353


title: HaCaT, p63 enhancer library, replicate 1, RNA

value: HaCaT


title: melanoma_FFPE_190 [20191219_Karen4_01_07]

value: F

value: IIA

tag: breslow thickness

value: Alive

value: primary cutaneous melanoma tissue


title: K562, wtLSD1GFP_antiH3K14ac-rep2,CUT&RUN


title: melanoma_FFPE_191 [20191219_Karen4_01_08]

value: M

value: IIC

tag: ulceration


title: K562, wtLSD1GFP_antiH3K14ac-rep1,CUT&RUN


title: melanoma_FFPE_187 [20191219_Karen4_01_04]

tag: os


title: K562, Y391K-LSD1GFP_antiIgG-rep1,CUT&RUN


title: K562, Y391K-LSD1GFP_antiH3K4me2-rep1,CUT&RUN

value: Abcam, #ab32356


title: melanoma_FFPE_186 [20191219_Karen4_01_03]

value: Present

tag: pfs


title: K562, wtLSD1GFP_antiH3K4me2-rep2,CUT&RUN

value: human immportalized chronic myelogenous leukemia


title: melanoma_FFPE_188 [20191219_Karen4_01_05]

tag: dead or alive at last contact

value: Dead


title: melanoma_FFPE_185 [20191219_Karen4_01_02]

tag: tag


title: K562, wtLSD1GFP_antiH3K4me2-rep1,CUT&RUN

tag: cell line

value: parental wtLSD1-GFP


title: K562, Y391K-LSD1GFP_antiH3K4me1-rep2,CUT&RUN

value: Epicypher, #13-0040


title: melanoma_FFPE_184 [20191219_Karen4_01_01]

value: Columbia

value: IIIA


title: melanoma_FFPE_181 [20191213_Karen3_01_10]

value: Absent


title: melanoma_FFPE_182 [20191213_Karen3_01_11]


title: K562, Y391K-LSD1GFP_antiH3K4me1-rep1,CUT&RUN


title: K562, wtLSD1GFP_antiH3K4me1-rep2,CUT&RUN


title: K562, Y391K-LSD1GFP_antiH3K14ac-rep1,CUT&RUN

value: Millipore Sigma, #07-353


title: melanoma_FFPE_189 [20191219_Karen4_01_06]


title: K562, wtLSD1GFP_antiH3K4me1-rep1,CUT&RUN


title: melanoma_FFPE_179 [20191213_Karen3_01_08]


title: K562, Y391K-LSD1GFP_antiGFP-rep2,CUT&RUN

value: Abcam, #ab290


title: melanoma_FFPE_177 [20191213_Karen3_01_06]


title: melanoma_FFPE_180 [20191213_Karen3_01_09]

value: IIB


title: K562, wtLSD1GFP_antiGFP-rep1,CUT&RUN

value: Abcam,  #ab290


title: K562, Y391K-LSD1GFP_antiH3K4me2-rep2,CUT&RUN


title: Plasmid pool, replicate 2, DNA

description: PCR amplified plasmid DNA (STARR-seq DNA)

library_source: other

molecule: other

organism: synthetic construct


title: Plasmid pool, replicate 1, DNA


title: melanoma_FFPE_175 [20191213_Karen3_01_04]

value: IIA

value: Alive


title: melanoma_FFPE_176 [20191213_Karen3_01_05]

value: M

value: primary cutaneous melanoma tissue


title: melanoma_FFPE_183 [20191213_Karen3_01_12]


title: HCT116_KO_rep1

city: Houston

first: Catherine

last: Denicourt

state: TX

address: 6431 Fannin St

department: Integrative Biology and Pharmacology

institute: The University of Texas HSC Houston

description: purified tRNA isolated from total RNA were sequenced

data_processing:
The bulk files were saved during sequencing for subsequent simulation runs using the alternative configuration described by Lucas et al. (Nature Biotechnology, 2024, 42, 72–86). Fastq files generated by the simulation run were aligned to high confidence mature tRNA sequences retrieved from GtRNAdb using the bwa alignment tool with parameters set as follows: -W 13 -k 6 -x ont2d -T20. Sequence alignments in bam files were extracted by BEDTools. One tRNA gene was selected for each iso-decoder based on the read counts in this alignment to generate a reference file containing only one gene per tRNA iso-decoder. Differential expression of tRNAs was analyzed by aligning the fastq files to the one iso-decoder reference with the bwa alignment tool, using parameters set as follows: -W 13 -k 6 -x ont2d -T20, and extracting the alignment read counts by BEDTools. Mismatches, insertions and deletions at each position of tRNA iso-decoders were extracted using Samtools.
Assembly: tRNA sequences retrieved from GtRNAdb
Supplementary files format and content: excel workbook file containing basecalling errors of each position of tRNA in Nano-tRNAseq.
Library strategy: Nano-tRNAseq

growth_protocol: WT and TRMT1L KO HCT116 cells were cultured under 5% CO2 atmosphere at 37°C in high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplement with 5% fetal bovine serum (FBS) and 100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol reagent following manufacturer’s instructions. tRNAs were isolated from total RNA by ion exchange chromatography. The RNA samples were brought to a final concentration of 20 mM HEPES-KOH (pH 7.5) and loaded onto a Bio-Rad EconoFit Macro-Prep DEAE columns (BioRad, 12009274) pre-equilibrated sequentially with the following buffers: 6 column volumes (CV) of low salt buffer (200 mM NaCl, 8 mM MgCl2, 20 mM HEPES-KOH pH 7.5), followed by 15 CV of high salt buffer (450 mM NaCl, 16 mM MgCl2, 20 mM HEPES-KOH pH 7.5), then 15 CV of low salt buffer, and finally, 15 CV of binding buffer (100 mM NaCl, 20 mM HEPES-KOH pH 7.5). After loading the RNA, the column was washed with 10 CV of binding buffer and eluted with a step gradient of 200 mM NaCl, 8 mM MgCl2, 20 mM HEPES-KOH to 500 mM NaCl, 16 mM MgCl2, 20 mM HEPES-KOH. A final elution step was conducted with 1 M NaCl. After elution, the collected fractions were analyzed by on urea-PAGE, and the fractions containing pure tRNA were pooled and subsequently recovered by precipitation with 1/10 volume of 3M sodium acetate (pH 5.2), 20 ug/ml Glycogen and 1.5 volume of isopropanol.
The tRNA samples purified from total RNA were prepared into libraries following the Nano-tRNAseq protocol developed by Lucas et al. (Nature Biotechnology, 2024, 42, 72–86). Initially, the tRNAs were deacylated in 100 mM Tris-HCl (pH 9.0) at 37°C for 30 minutes. After recovery using the NEB RNA Cleanup kit, the tRNAs were ligated to pre-annealed 5' and 3' splint adaptors (5’ RNA splint adapter: 5’-rCrCrUrArArGrArGrCrArArGrArArGrArArGrCrCrUrGrGrN, 3’ splint adapter: 5’-Phos-rGrGrCrUrUrCrUrUrCrUrUrGrCrUrCrUrUrArGrGrArArArArArArArArArAAAA-3’) with T4 RNA 2 Ligase followed by purification on AMPure RNAClean XP beads. The splint adaptor-ligated tRNAs were reverse transcribed using SuperScript IV Reverse Transcriptase at 60 °C for 1 hour followed by 85 °C for 5 minutes to linearize the tRNAs. The linearized tRNAs were cleaned up with AMPure RNAClean XP beads and then prepared into libraries following the standard protocol of the Direct RNA Sequencing Kit (SQK-RNA002) before being sequenced on a MinION flow cell (FLO-MIN-106).

value: human colorectal carcinoma cell line

tag: genotype

value: TRMT1L KO


title: HCT116_KO_rep2

tag: cell type


title: melanoma_FFPE_171 [20191213_Karen2_01_12]

city: New York

value: F

value: Present


title: melanoma_FFPE_173 [20191213_Karen3_01_02]

value: Dead


title: melanoma_FFPE_170 [20191213_Karen2_01_11]


title: melanoma_FFPE_172 [20191213_Karen3_01_01]


title: HCT116_WT_rep1

value: WT


title: melanoma_FFPE_169 [20191213_Karen2_01_10]

value: Columbia

value: IIC


title: melanoma_FFPE_174 [20191213_Karen3_01_03]

value: Absent


title: melanoma_FFPE_168 [20191213_Karen2_01_09]


title: K562, wtLSD1GFP_antiGFP-rep2,CUT&RUN

value: human immportalized chronic myelogenous leukemia

tag: cut&run antibody

value: parental wtLSD1-GFP


title: K562, Y391K-LSD1GFP_antiGFP-rep1,CUT&RUN

value: Abcam, #ab290

tag: treatment


title: melanoma_FFPE_178 [20191213_Karen3_01_07]

tag: gender

value: IIIB


title: E14.5 knockout MEFs, replicate 4

city: Ottawa

first: Balwant

last: Tuana

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
Reads were assigned to theGRCm38_GENCODE M25 using Salmon and the differential expression of transcripts was analysed by DESeq2.
The nf-core/rnaseq pipeline version 3.11.2 was used to generate the quality assessment and read pseudocounts table
Assembly: Analysis was performed using GENCODE M25 annotations and the GRCm38 genome assembly.
Supplementary files format and content: KO_vs_WT_FC, a .txt file containing the log2FoldChange in gene expression comparing knockout and wild type cells.
Supplementary files format and content: report_rnaseq_gene_230602, a html file containing the description of the RNA-sequencing analysis
Supplementary files format and content: salmon.merged.gene_counts_length_scaled, a .tsv file containing gene counts.

source_name: Mouse embryonic fibroblasts

growth_protocol: Plug-checked females underwent c-section to harvest E14.5 embryos. Tails were taken for genotyping. Head and organs were removed, and the remaining body was utilize for MEFs isolation.MEFs were cultured in a medium containing high glucose DMEM (Wisent, cat# 319-005), 1x MEM (Gibco, cat# 11140050), 20 mM HEPES, 10% fetal bovine serum (FBS) (Wisent, cat# 080-150), 1x antibiotic-antimycotic (Gibco, cat# 15240062) and 0.1 mM β-mercaptoethanol, and kept in humidified atmosphere with 5% CO2 and at 37°C.

extract_protocol:
Total RNA was extracted from the cells using RNeasy mini kit (QIAGEN) according to manufacturer protocols.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: After passage 2, cells were transfected with SV40 large T antigen. Immortalization was achieved after at least 5 splits of 1/10 or until cellular senescence was no longer observed.

tag: strain

tag: developmental stage

value: embryonic day E14.5

value: Mouse embryonic fibroblasts

value: SLMAP3 knockout

value: immortalized with SV40 large T antigen


title: E14.5 wildtype MEFs, replicate 4

value: Wildtype


title: melanoma_FFPE_167 [20191213_Karen2_01_08]

value: M

tag: age at diagnosis

tag: cohort

value: IIIA

value: primary cutaneous melanoma tissue


title: E14.5 wildtype MEFs, replicate 3


title: E14.5 knockout MEFs, replicate 2


title: melanoma_FFPE_166 [20191213_Karen2_01_07]

tag: stage at original diagnosis

value: IIB

tag: ajcc thickness

value: Present

value: Dead


title: E14.5 knockout MEFs, replicate 1


title: melanoma_FFPE_164 [20191213_Karen2_01_05]

value: Columbia

tag: breslow thickness

tag: ulceration

value: Alive


title: HCT116_WT_rep2

value: human colorectal carcinoma cell line

value: WT


title: E14.5 wildtype MEFs, replicate 2


title: E14.5 wildtype MEFs, replicate 1


title: melanoma_FFPE_162 [20191213_Karen2_01_03]

value: F

value: IIA

tag: os

tag: pfs


title: E. coli + tagged yfif, replicate 3, CL

city: Cambridge

first: Mie

last: Monti

email: miemtir@gmail.com, mm2073@cam.ac.uk

address: MRC Toxicology Unit, Tennis Ct Rd, Cambridge CB2 1QR

country: United Kingdom

institute: MRC Toxicology Unit

description: iCLIP enriched RNA

data_processing:
Reads were demultiplexed with iCount (version 2.0.0) demulitplex function
Artificial genome created by masking rRNA and tRNA sequences in E. coli str. K-12 substr. MG1655 genome assembly (GCF_000005845.2 ASM584v2). The fasta sequences for the rRNA/tRNA entries were then clusterised to consensus motifs (>70% sequence similarity) using vsearch (version 2.15.2). The resulting sequences were appended to the masked genome as separate chromosomes.
Wobble bases remaining from adapter at the 5' end removed with cutadapt (version 3.4)
Demultiplexed reads were mapped to an artificial E. coli genome with STAR (version2.7.10b) --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNover 0.3 --alignEndsType EndToEnd
Aligned reads deduplicated with UMITools (version 1.1.2)
Enriched regions to the masked genome were detected with iCount (version 2.0.0) clusters. Enriched regions to the scaffold regions were detected using PureCLIP (version 1.3.1) using the negative samples as the input control for the model.
Assembly: GCF_000005845.2 ASM584v2 (modified, see data processing steps)
Supplementary files format and content: PureCLIP peaks (.bedgraph)
Supplementary files format and content: iCount peaks (.bedgraph)
Library strategy: iCLIP-seq

organism: Escherichia coli

source_name: E. coli

growth_protocol: Bacterial strains transformed with tagged protein of interest (see below ‘Bacterial N-terminal epitope tagging’) as well as a wildtype (WT) strain were grown in M9LB bacterial growth media at 37°C under low light conditions and constant shaking (250 RPM). Media prepared with 15.6 g M9 minimal media salts 5X (Sigma-Aldrich), 10 mL glucose 20% (w/v), 1 mL MgSO4.7H20 (1M), 1 mL thiamine hydrochloride (1 mg/mL), 1 mL CaCl2 (1M) in 1 L purified water. Media was supplemented with 10% v/v LB (lysogeny broth) . Final pH 7.0 at 25°C.

extract_protocol:
Cells were mechanically lysed with glass beads in CLIP lysis buffer. The suspension was cleared once and sonicated on low for 10 cycles (30 s on/off). RNA was partially digested with RNase I prior to immunoprecipitation of the protein of interest. Crosslinked RNA was 3' end dephosphorylated and ligated with a fluorescent adaptor on the beads prior to SDS-PAGE and nitrocellulose transfer. Relevant sections of the membrane were cut out, dissolved and the RNA released by proteinase K treatment.
Enriched RNA was reverse transcibed with SSIV (Invitrogen) and treated with RNase H (NEB). cDNA was then column-purified and circularised with circLigase (Epicentre/Illumina) for 2 hrs. Circularised cDNA was directly PCR amplified and quantified with Bioanlayzer prior to sequencing.

treatment_protocol: Proteins of interest were amplified by PCR from E. coli DH5ɑ and inserted into the expression vector pBADcLIC42 by recombination-based cloning which introduces a C-terminal tag (-ENLYFQGHHHHHHHHHH). The resulting plasmids were then transformed into E. coli DH5ɑ. Strains were induced with 0.01% L-arabinose at the exponential phase (OD ~0.4) and harvested at stationary phase and irradiated with UV-C light for the cross-linked samples (CL) or directly pelleted for the non-cross-linked (NC). Here, the WT strain was the negative control and was UV-irradiated.

value: E. coli

value: + yfif tagged plasmid

value: CL


title: E. coli + tagged yfif, replicate 2, CL

description: iCLIP enriched RNA


title: E. coli + tagged yfif, replicate 1, CL

description: iCLIP enriched RNA


title: melanoma_FFPE_160 [20191213_Karen2_01_01]

value: Absent

tag: dead or alive at last contact

tag: tag


title: melanoma_FFPE_161 [20191213_Karen2_01_02]


title: E14.5 knockout MEFs, replicate 3

value: embryonic day E14.5

value: Mouse embryonic fibroblasts

tag: genotype

value: SLMAP3 knockout

value: immortalized with SV40 large T antigen


title: melanoma_FFPE_158 [20191212_karen1_01_11]

value: M

value: IIB

value: primary cutaneous melanoma tissue


title: melanoma_FFPE_159 [20191212_karen1_01_12]

value: Columbia


title: E. coli + tagged yfif, negative control, NC

description: iCLIP enriched RNA

tag: cell type

value: NC


title: E. coli + tagged htpg, replicate 2, CL

description: iCLIP enriched RNA

value: + htpG tagged plasmid


title: S11_50_BPA_male

city: Melbourne

first: Wah Chin

last: Boon

state: Victoria

address: 30 Royal Parade Parkville

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

data_processing:
The libraries were sequenced with 50bp single end reads using an Illumina Miseq and read quality assessed using FastQC.
The sequence reads were then aligned against the Mus musculus genome (Build version GRCm38).   The Tophat aligner (v2.0.14) was used to map reads to the genomic sequences
Sequencing data was then summarized into reads per transcript using Feature counts and the transcripts were assembled with the StringTie tool v1.2.4 using the reads alignment with Mus_musculus.GRCm38 and reference annotation based assembly option (RABT) using the Gencode gene models for the mouse GRCm38/mm10 genome build.
Normalisation and statistical analysis on the count data was executed using EdgeR (version edgeR_3.14.2 in R studio, R version 3.14.2).
The data was scaled using trimmed mean of M-values (TMM).
Assembly: mouse GRCm38/mm10
Supplementary files format and content: csv file includes raw counts for each sample

source_name: brain cortex

extract_protocol:
Total RNA was extracted using PARIS kit (Invitrogen) according to protocol supplied by the manufacturer
cDNA libraries were generated using the SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing kit (Agilent Technologies), according to manufacturer’s instructions.

tag: tissue

value: brain cortex

tag: age

value: WT, SRY +

value: 50ug/kg BPA

tag: fetal id


title: E. coli + tagged htpg, replicate 1, CL

description: iCLIP enriched RNA

value: E. coli

tag: treatment


title: melanoma_FFPE_165 [20191213_Karen2_01_06]

tag: gender

value: IIA

value: Dead


title: melanoma_FFPE_157 [20191212_karen1_01_10]

tag: age at diagnosis

value: Present

value: Alive


title: E. coli WT, negative control, CL (cross-link)

description: iCLIP enriched RNA

value: WT

value: CL


title: melanoma_FFPE_163 [20191213_Karen2_01_04]

value: F

tag: cohort

value: IIIB

value: Absent


title: melanoma_FFPE_156 [20191212_karen1_01_09]

value: M

tag: stage at original diagnosis

value: IIB

value: primary cutaneous melanoma tissue


title: E. coli + tagged htpg, negative control, NC (non-cross-link)

description: iCLIP enriched RNA

value: + htpG tagged plasmid

value: NC


title: S7_50_BPA_male

tag: strain

value: brain cortex

value: WT, SRY +


title: melanoma_FFPE_152 [20191212_karen1_01_05]

value: Columbia

tag: ajcc thickness

tag: breslow thickness


title: melanoma_FFPE_155 [20191212_karen1_01_08]

value: IIA

tag: ulceration

tag: os


title: melanoma_FFPE_154 [20191212_karen1_01_07]

tag: pfs

tag: dead or alive at last contact

value: Dead


title: melanoma_FFPE_153 [20191212_karen1_01_06]

value: Present

tag: tag


title: melanoma_FFPE_151 [20191212_karen1_01_04]

value: Alive


title: melanoma_FFPE_150 [20191212_karen1_01_03]


title: melanoma_FFPE_149 [20191212_karen1_01_02]


title: S6_0_BPA_male

tag: genotype

value: vehicle (peanut oil)


title: melanoma_FFPE_148 [20191212_karen1_01_01]


title: S2_0_BPA_male

tag: tissue


title: JK4_1_PCR2_1_3_R8

city: Crawley

first: Jonathan

last: Chee

state: WA

address: M503, 35 Stirling Highway

institute: University of Western Australia

data_processing:
Agilent TapeStation for quality control of DNA integrity.
Paired-end (2 × 300 bp) high-throughput sequencing was performed using the Illumina MiSeq platform.
Data processing, aggregation of UMIs and alignment of CDR3 sequences to the IMGT/V-QUEST reference genome were performed using repertoire analysis software based on MIGEC and MiXCR pipelines. Only sequences with UMIs were aligned.
TCRβ clones (defined by the CDR3 amino acid sequence) were excluded if they were less than 8 or greater than 20 amino acids in length, included a stop codon or a frameshift.
Assembly: IMGT/V-QUEST reference genome
Supplementary files format and content: txt files
Supplementary files format and content: clonotype tables
Library strategy: TCR-seq

source_name: Tumour

extract_protocol:
Sorted cells were stored at -80C. RNA was extracted from frozen cells using the RNeasy Plus Micro Kit.
TCRβ amplicon libraries were generated with 5’Rapid Amplification of cDNA Ends (5’RACE) technology. RNA was transcribed to cDNA with a TCRβ constant region primer and a modified SMARTerIIA primer (Integrated DNA Technologies), with 9nt long unique molecular identifiers (UMI) added to individual TCRβ cDNA sequences. TCRβ locus was amplified by nested PCR with an additional TCRβ constant region primers, and a universal primer to SMARTerIIA, with the final PCR adding sequencing adaptors and barcodes to the TCRβ libraries. Products after each PCR were purified using AMPure XP AgenCourt Beads (Beckman Coulter).

treatment_protocol: Whole tumours were surgically excised from mice

value: BALB/c

value: Tumour

tag: cell type

tag: timepoint

value: day 13


title: melanoma_cell_line_12 [20180516_Karen01_K01_12]

source_name: melanoma cell line_YUCHIME

value: Yale

tag: tnm


title: JK4_1_PCR2_1_3_L8


title: JK4_1_PCR2_1_3_R4


title: melanoma_cell_line_9 [20180516_Karen01_K01_09]

source_name: melanoma cell line_WM1552C

tag: gender

value: M

value: Wistar


title: melanoma_cell_line_10 [20180516_Karen01_K01_10]

source_name: melanoma cell line_YUPEET

tag: age at diagnosis

value: primary cutaneous melanoma tissue


title: S3_50_BPA_male

tag: age

tag: treatment

value: 50ug/kg BPA

tag: fetal id


title: JK4_1_PCR2_1_3_L4

tag: strain


title: JK4_1_PCR2_1_2_L4


title: JK4_1_PCR2_1_2_R8


title: melanoma_cell_line_8 [20180516_Karen01_K01_08]

source_name: melanoma cell line_WM115A

value: F

tag: cohort

tag: stage at original diagnosis

tag: ajcc thickness

tag: breslow thickness


title: JK4_1_PCR2_1_2_L8


title: JK4_1_PCR2_1_2_R4


title: melanoma_cell_line_7 [20180516_Karen01_K01_07]

source_name: melanoma cell line_WM902B

tag: ulceration

tag: os

tag: pfs

tag: dead or alive at last contact


title: JK4_1_PCR2_1_0_R4

tag: tissue

tag: cell type


title: melanoma_cell_line_5 [20180516_Karen01_K01_05]

source_name: melanoma cell line_WM983A

tag: tnm

tag: tag


title: melanoma_cell_line_3 [20180516_Karen01_K01_03]

source_name: melanoma cell line_WM793

tag: gender

tag: age at diagnosis


title: S9_0_BPA_male

value: brain cortex

tag: age

tag: genotype

tag: treatment


title: melanoma_cell_line_6 [20180516_Karen01_K01_06]

source_name: melanoma cell line_WM853

tag: cohort


title: melanoma_cell_line_2 [20180516_Karen01_K01_02]

source_name: melanoma cell line_WM278

tag: stage at original diagnosis


title: JK4_1_PCR2_1_0_R8

tag: strain

tag: timepoint


title: JK4_1_PCR2_1_0_L8


title: JK4_1_PCR2_1_0_L4


title: melanoma_cell_line_4 [20180516_Karen01_K01_04]

source_name: melanoma cell line_WM39

tag: ajcc thickness

tag: breslow thickness

tag: ulceration


title: melanoma_FFPE_147 [20181219_Karen04_K01_12]

source_name: primary melanoma FFPE tissue

value: Moffitt

value: Absent

tag: os

tag: pfs

tag: dead or alive at last contact


title: melanoma_cell_line_1 [20180516_Karen01_K01_01]

source_name: melanoma cell line_WM35

tag: tnm


title: RENCA_020_NR_8

tag: tissue

tag: cell type

value: RENCA

value: day  0


title: melanoma_FFPE_146 [20181219_Karen04_K01_11]

tag: gender

tag: age at diagnosis

value: IIA

tag: tag


title: melanoma_cell_line_11 [20180516_Karen01_K01_11]

source_name: melanoma cell line_WW165


title: RENCA_014_RS_7


title: melanoma_FFPE_145 [20181219_Karen04_K01_10]

value: Dead


title: RENCA_012_RS_5


title: RENCA_013_RS_6


title: RENCA_002_NR_1


title: RENCA_011_RS_4


title: melanoma_FFPE_144 [20181219_Karen04_K01_09]

value: IIB

value: Present


title: melanoma_FFPE_143 [20181219_Karen04_K01_08]

value: IIIC

value: Alive


title: RENCA_008_NR_2

value: BALB/c

value: Tumour


title: melanoma_FFPE_140 [20181219_Karen04_K01_05]

value: IB


title: melanoma_FFPE_139 [20181219_Karen04_K01_04]

value: M

value: primary cutaneous melanoma tissue


title: melanoma_FFPE_141 [20181219_Karen04_K01_06]


title: RENCA_010_NR_3


title: AB1_653_RS_10

value: day  6


title: AB1_654_NR_4


title: AB1_655_RS_11


title: AB1_656_NR_12


title: AB1_649_RS_9


title: melanoma_FFPE_142 [20181219_Karen04_K01_07]


title: melanoma_FFPE_137 [20181219_Karen04_K01_02]


title: melanoma_FFPE_135 [20181211_Karen03_K01_12]

value: F


title: melanoma_FFPE_134 [20181211_Karen03_K01_11]

value: Moffitt


title: melanoma_FFPE_136 [20181219_Karen04_K01_01]

value: Absent


title: melanoma_FFPE_133 [20181211_Karen03_K01_10]


title: melanoma_FFPE_138 [20181219_Karen04_K01_03]

value: IIIB


title: AB1_641_NR_3


title: melanoma_FFPE_132 [20181211_Karen03_K01_09]


title: AB1_640_NR_2


title: AB1_638_NR_1


title: melanoma_FFPE_131 [20181211_Karen03_K01_08]


title: AB1_623_RS_8


title: AB1_621_NR_7


title: melanoma_FFPE_130 [20181211_Karen03_K01_07]


title: AB1_610_RS_12


title: melanoma_FFPE_129 [20181211_Karen03_K01_06]


title: AB1_611_RS_6


title: AB1_608_RS_5


title: melanoma_FFPE_128 [20181211_Karen03_K01_05]


title: AB1_453_RS_8

value: day  4


title: melanoma_FFPE_127 [20181211_Karen03_K01_04]


title: melanoma_FFPE_126 [20181211_Karen03_K01_03]


title: AB1_607_RS_11


title: AB1_603_NR_9


title: melanoma_FFPE_124 [20181211_Karen03_K01_01]

value: IIIA


title: AB1_449_NR_12


title: melanoma_FFPE_125 [20181211_Karen03_K01_02]


title: melanoma_FFPE_123 [20181207_Karen02_K01_12]

value: IIA


title: AB1_450_NR_7


title: melanoma_FFPE_122 [20181207_Karen02_K01_11]

value: Dead


title: AB1_435_NR_11


title: AB1_426_RS_6


title: AB1_430_NR_10


title: melanoma_FFPE_119 [20181207_Karen02_K01_08]

value: Present


title: melanoma_FFPE_117 [20181207_Karen02_K01_06]

value: IIB


title: melanoma_FFPE_121 [20181207_Karen02_K01_10]


title: melanoma_FFPE_118 [20181207_Karen02_K01_07]

value: Alive


title: melanoma_FFPE_120 [20181207_Karen02_K01_09]


title: AB1_424_RS_5

value: BALB/c


title: AB1_423_RS_4

value: Tumour


title: melanoma_FFPE_116 [20181207_Karen02_K01_05]


title: melanoma_FFPE_114 [20181207_Karen02_K01_03]

value: IB


title: AB1_418_NR_3


title: AB1_415_NR_2


title: AB1_604_NR_10


title: melanoma_FFPE_113 [20181207_Karen02_K01_02]


title: AB1_414_NR_9


title: melanoma_FFPE_112 [20181207_Karen02_K01_01]

value: M


title: AB1_410_RS_7


title: AB1_411_RS_8


title: AB1_406_RS_6


title: AB1_407_RS_1


title: melanoma_FFPE_111 [20181206_Karen01_K01_12]

value: primary cutaneous melanoma tissue


title: AB1_401_NR_5


title: melanoma_FFPE_109 [20181206_Karen01_K01_10]


title: AB1_239_RS_4

value: day  2


title: melanoma_FFPE_108 [20181206_Karen01_K01_09]

value: IIIC


title: AB1_234_RS_1


title: melanoma_FFPE_107 [20181206_Karen01_K01_08]

value: Moffitt


title: melanoma_FFPE_104 [20181206_Karen01_K01_05]

value: Absent


title: melanoma_FFPE_106 [20181206_Karen01_K01_07]


title: melanoma_FFPE_115 [20181207_Karen02_K01_04]


title: melanoma_FFPE_103 [20181206_Karen01_K01_04]

value: IIIB


title: AB1_237_RS_3


title: melanoma_FFPE_110 [20181206_Karen01_K01_11]


title: AB1_232_NR_12


title: melanoma_FFPE_105 [20181206_Karen01_K01_06]


title: melanoma_FFPE_102 [20181206_Karen01_K01_03]

value: F


title: melanoma_FFPE_101 [20181206_Karen01_K01_02]


title: AB1_231_RS_7


title: AB1_229_NR_11


title: melanoma_FFPE_100 [20181206_Karen01_K01_01]


title: melanoma_FFPE_99 [20180314_Karen02_K13_12]


title: AB1_228_RS_6


title: melanoma_FFPE_98 [20180314_Karen02_K13_11]


title: AB1_227_NR_10


title: AB1_225_NR_5


title: melanoma_FFPE_97 [20180314_Karen02_K13_10]


title: melanoma_FFPE_96 [20180314_Karen02_K13_09]


title: AB1_235_RS_2


title: AB1_233_RS_8


title: AB1_223_NR_4


title: AB1_221_NR_3


title: melanoma_FFPE_95 [20180314_Karen02_K13_08]

value: IIC


title: melanoma_FFPE_94 [20180314_Karen02_K13_07]


title: AB1_205_RS_2


title: melanoma_FFPE_93 [20180314_Karen02_K13_06]


title: AB1_202_NR_1


title: melanoma_FFPE_92 [20180314_Karen02_K13_05]


title: AB1_038_NR_2

value: day  0


title: AB1_024_RS_7


title: AB1_027_RS_9


title: melanoma_FFPE_91 [20180314_Karen02_K13_04]


title: AB1_025_NR_8


title: AB1_018_NR_1


title: melanoma_FFPE_89 [20180314_Karen02_K13_02]

value: Dead


title: AB1_022_RS_6


title: melanoma_FFPE_90 [20180314_Karen02_K13_03]

value: Present


title: melanoma_FFPE_88 [20180314_Karen02_K13_01]


title: AB1_013_NR_5


title: melanoma_FFPE_85 [20180314_Karen01_K01_10]

value: IIB


title: melanoma_FFPE_87 [20180314_Karen01_K01_12]


title: AB1_226_NR_9


title: melanoma_FFPE_84 [20180314_Karen01_K01_09]


title: AB1_057_NR_4


title: melanoma_FFPE_86 [20180314_Karen01_K01_11]

value: IIA


title: AB1_047_NR_12

value: BALB/c


title: AB1_044_RS_11

value: Tumour


title: melanoma_FFPE_82 [20180314_Karen01_K01_07]

value: Alive


title: melanoma_FFPE_81 [20180314_Karen01_K01_06]

value: M


title: melanoma_FFPE_80 [20180314_Karen01_K01_05]

value: primary cutaneous melanoma tissue


title: melanoma_FFPE_83 [20180314_Karen01_K01_08]


title: melanoma_FFPE_78 [20180314_Karen01_K01_03]

value: II


title: AB1_037_RS_10


title: melanoma_FFPE_79 [20180314_Karen01_K01_04]

value: IIIC


title: melanoma_FFPE_77 [20180314_Karen01_K01_02]

value: Moffitt


title: melanoma_FFPE_76 [20180314_Karen01_K01_01]

value: Absent


title: 629_NR_5

value: RENCA

value: day  6


title: AB1_006_RS_9


title: melanoma_FFPE_75 [20180213_Karen04_K04_43]


title: AB1_010_RS_10


title: 625_RS_3


title: AB1_011_NR_11


title: 624_NR_2


title: 623_RS_12


title: AB1_050_NR_3


title: melanoma_FFPE_74 [20180213_Karen04_K04_41]


title: melanoma_FFPE_72 [20180213_Karen04_K04_37]


title: melanoma_FFPE_71 [20180213_Karen03_K03_36]

value: F

value: Sinai


title: melanoma_FFPE_70 [20180213_Karen03_K03_35]

value: IIC

value: Dead


title: 614_NR_10


title: 620_RS_11


title: melanoma_FFPE_73 [20180213_Karen04_K04_39]

value: Present


title: AB1_017_RS_12

value: day  0


title: 612_NR_9

value: BALB/c


title: melanoma_FFPE_67 [20180213_Karen03_K03_32]

value: IIA


title: 602_RS_7

value: Tumour


title: 605_RS_8


title: melanoma_FFPE_68 [20180213_Karen03_K03_33]

value: IIB


title: melanoma_FFPE_66 [20180213_Karen03_K03_31]

value: Alive

value: primary cutaneous melanoma tissue


title: 601_NR_6


title: 437_NR_5

value: day  4


title: melanoma_FFPE_65 [20180213_Karen03_K03_30]

value: M


title: 436_RS_4


title: 432_RS_3


title: melanoma_FFPE_63 [20180213_Karen03_K03_28]

value: IIIC


title: melanoma_FFPE_62 [20180213_Karen03_K03_27]

value: Absent


title: melanoma_FFPE_69 [20180213_Karen03_K03_34]

value: IB


title: 428_NR_2

value: RENCA


title: melanoma_FFPE_59 [20180208_Karen02_K02_24]

value: Sinai


title: melanoma_FFPE_58 [20180208_Karen02_K02_23]


title: melanoma_FFPE_61 [20180213_Karen03_K03_26]

value: IV


title: melanoma_FFPE_57 [20180208_Karen02_K02_22]

value: F


title: melanoma_FFPE_56 [20180208_Karen02_K02_21]

value: Present


title: melanoma_FFPE_64 [20180213_Karen03_K03_29]


title: 426_NR_11


title: 424_RS_10


title: melanoma_FFPE_54 [20180208_Karen02_K02_19]

value: IIC

value: Dead


title: melanoma_FFPE_55 [20180208_Karen02_K02_20]


title: melanoma_FFPE_53 [20180208_Karen02_K02_18]


title: melanoma_FFPE_52 [20180208_Karen02_K02_17]


title: melanoma_FFPE_51 [20180208_Karen02_K02_16]


title: melanoma_FFPE_50 [20180208_Karen02_K02_15]


title: melanoma_FFPE_60 [20180213_Karen03_K03_25]

value: IIA


title: Caco2Expression_Caco2_withS_Typhimurium_120mins_Rep2

city: Davis

first: Bart

last: Weimer

address: 1 Shields Ave

institute: UC Davis

hyb_protocol: An aliquot of 500ng for pure culture and 2,000ng for coculture was hybridized onto the respective chips.

scan_protocol: 3,000 GeneChip Scanner with Autoloader (Affymetrix). All samples were proceesed according to Affymetrix protocols.

data_processing: Raw data (.cel files) were background corrected, quantile normalized and summarized using RMA (Irizarry et al., 2003).

label: biotin

source_name: Caco2 expression after 120 mins incubation with S. Typhimurium

label_protocol: Fragmented cDNA was labeled using GeneChip DNA Labeling reagent (Affymetrix) and Terminal Transferase enzyme (NEB) as per manufacturers' reccomendation by using 2uL GeneChip labeling reagent and 3uL TdT/ug cDNA at 37˚C for 60min.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: ATCC

value: ATTC HTB-37

tag: cell line

value: Human colonic epithelial cells (Caco2)

tag: treatment

value: 120 mins incubation with S. Typhimurium


title: Caco2Expression_Caco2_withS_Typhimurium_1200mins_Rep1


title: Caco2Expression_Caco2_withS_Typhimurium_90mins_Rep2

source_name: Caco2 expression after 90 mins incubation with S. Typhimurium

value: 90 mins incubation with S. Typhimurium


title: Caco2Expression_Caco2_withS_Typhimurium_60mins_Rep2

source_name: Caco2 expression after 60 mins incubation with S. Typhimurium

value: 60 mins incubation with S. Typhimurium


title: 422_NR_8

source_name: Tumour

tag: strain

value: BALB/c

value: Tumour

value: day  4


title: 430_RS_12

tag: timepoint


title: Caco2Expression_Caco2_withS_Typhimurium_60mins_Rep1


title: melanoma_FFPE_49 [20180208_Karen02_K02_14]

tag: cohort

tag: stage at original diagnosis

tag: ajcc thickness

value: Absent

value: Alive

value: primary cutaneous melanoma tissue


title: Caco2Expression_Caco2_withS_Typhimurium_90mins_Rep1


title: melanoma_FFPE_48 [20180208_Karen02_K02_13]

value: M

value: Sinai

value: IV

tag: breslow thickness

tag: ulceration

tag: os


title: melanoma_FFPE_47 [20180208_Karen01_K01_12]

tag: tnm

tag: pfs

tag: dead or alive at last contact


title: 421_NR_7

tag: tissue

tag: cell type

value: RENCA


title: 423_NR_9


title: 420_RS_6


title: Caco2Expression_Caco2_withS_Typhimurium_30mins_Rep1

source_name: Caco2 expression after 30 mins incubation with S. Typhimurium

value: 30 mins incubation with S. Typhimurium


title: melanoma_FFPE_46 [20180208_Karen01_K01_11]

tag: gender

tag: age at diagnosis

value: Present

tag: tag


title: 406_RS_4


title: melanoma_FFPE_42 [20180208_Karen01_K01_07]

value: IB


title: melanoma_FFPE_43 [20180208_Karen01_K01_08]

value: F


title: 405_RS_3


title: 404_NR_2


title: melanoma_FFPE_39 [20180208_Karen01_K01_04]


title: melanoma_FFPE_40 [20180208_Karen01_K01_05]

value: IIIC


title: Caco2Expression_Caco2_withB_infantis_andS_Typhimurium_120mins_Rep1

source_name: Caco2 expression after 120 mins incubation with B. infantis and S. Typhimurium

tag: ATCC

value: ATTC HTB-37

tag: cell line

value: Human colonic epithelial cells (Caco2)

tag: treatment


title: melanoma_FFPE_44 [20180208_Karen01_K01_09]

tag: cohort


title: Caco2Expression_Caco2_withS_Typhimurium_30mins_Rep2


title: melanoma_FFPE_34 [20171110_Karen3_K33_09]

tag: stage at original diagnosis

value: IIC

value: Dead


title: melanoma_FFPE_37 [20180208_Karen01_K01_02]

tag: ajcc thickness


title: melanoma_FFPE_36 [20180208_Karen01_K01_01]

tag: breslow thickness


title: 412_RS_5

tag: strain

value: BALB/c

value: Tumour

tag: timepoint

value: day  4


title: 401_NR_1


title: Caco2Expression_Caco2_withB_infantis_andS_Typhimurium_60mins_Rep1

source_name: Caco2 expression after 60 mins incubation with B. infantis and S. Typhimurium


title: Caco2Expression_Caco2_withB_infantis_andS_Typhimurium_120mins_Rep2

value: 120 mins incubation with B. infantis and S. Typhimurium


title: melanoma_FFPE_45 [20180208_Karen01_K01_10]

tag: tnm

tag: ulceration

tag: os

value: primary cutaneous melanoma tissue


title: melanoma_FFPE_35 [20171110_Karen3_K36_12]

value: M

value: Sinai

value: Absent

tag: pfs

tag: dead or alive at last contact


title: Caco2Expression_Caco2_withB_infantis_andS_Typhimurium_60mins_Rep2

value: 60 mins incubation with B. infantis and S. Typhimurium


title: Caco2Expression_Caco2_withB_infantis_andS_Typhimurium_30mins_Rep2

source_name: Caco2 expression after 30 mins incubation with B. infantis and S. Typhimurium


title: melanoma_FFPE_32 [20171110_Karen3_K29_05]

tag: gender


title: Caco2Expression_Caco2_withB_infantis_andS_Typhimurium_30mins_Rep1

value: 30 mins incubation with B. infantis and S. Typhimurium


title: melanoma_FFPE_33 [20171110_Karen3_K30_06]

tag: age at diagnosis


title: Caco2Expression_Caco2_withB_infantis_120mins_Rep2

source_name: Caco2 expression after 120 mins incubation with B. infantis

value: 120 mins incubation with B. infantis


title: Caco2Expression_Caco2_withB_infantis_120mins_Rep1


title: 231_NR_11

tag: tissue

tag: cell type

value: RENCA

value: day  2


title: melanoma_FFPE_41 [20180208_Karen01_K01_06]

value: F

value: IB

tag: tag


title: 226_NR_10


title: 234_RS_12


title: melanoma_FFPE_31 [20171110_Karen3_K28_04]

value: Alive


title: 220_RS_9


title: melanoma_FFPE_30 [20171110_Karen3_K26_02]

value: IIB

value: Present


title: melanoma_FFPE_38 [20180208_Karen01_K01_03]


title: melanoma_FFPE_28 [20171109_Karen2_K22_10]

value: IIA


title: melanoma_FFPE_27 [20171109_Karen2_K21_09]


title: 217_RS_7

value: BALB/c

value: Tumour


title: 218_NR_8


title: melanoma_FFPE_26 [20171109_Karen2_K19_07]

value: primary cutaneous melanoma tissue


title: melanoma_FFPE_24 [20171109_Karen2_K14_02]


title: melanoma_FFPE_21 [20171109_Karen1_K10_10]

value: M

value: Dead


title: melanoma_FFPE_22 [20171109_Karen1_K11_11]

value: Sinai


title: 216_RS_6


title: melanoma_FFPE_29 [20171110_Karen3_K25_01]

value: Absent


title: melanoma_FFPE_18 [20171109_Karen1_K06_06]

value: IIID


title: melanoma_FFPE_19 [20171109_Karen1_K08_08]


title: melanoma_FFPE_20 [20171109_Karen1_K09_09]


title: Caco2Expression_Caco2_withB_infantis_30mins_Rep2

source_name: Caco2 expression after 30 mins incubation with B. infantis

tag: ATCC

value: ATTC HTB-37

tag: cell line

value: Human colonic epithelial cells (Caco2)

tag: treatment

value: 30 mins incubation with B. infantis


title: Caco2Expression_Caco2_withB_infantis_30mins_Rep1


title: Caco2Expression_Caco2_withB_infantis_60mins_Rep1

source_name: Caco2 expression after 60 mins incubation with B. infantis

value: 60 mins incubation with B. infantis


title: Caco2Expression_Caco2Alone_60mins_Rep2

source_name: Caco2 expression at 60 mins incubation, time matched to infection assays


title: Caco2Expression_Caco2Alone_120mins_Rep2

source_name: Caco2 expression at 120 mins incubation, time matched to infection assays


title: Caco2Expression_Caco2Alone_120mins_Rep1

value: 120 mins incubation, time matched to infection assays


title: 215_RS_1

value: RENCA

value: day  2


title: melanoma_FFPE_25 [20171109_Karen2_K16_04]

tag: cohort

tag: stage at original diagnosis

tag: ajcc thickness

value: Alive


title: melanoma_FFPE_23 [20171109_Karen2_K13_01]

value: F

value: IIIC

tag: breslow thickness

value: Present


title: melanoma_FFPE_14 [20170815_Karen02_K18_06]

tag: tnm

value: primary cutaneous melanoma tissue


title: melanoma_FFPE_16 [20170815_Karen02_K24_12]

value: M

value: IIC

tag: ulceration


title: melanoma_FFPE_17 [20171109_Karen1_K03_03]

value: Sinai

tag: os

value: Dead


title: 208_NR_2

tag: strain

value: BALB/c

value: Tumour

tag: timepoint


title: 212_NR_4


title: melanoma_FFPE_11 [20170815_Karen02_K15_03]

tag: gender

value: IIB

tag: pfs

tag: dead or alive at last contact


title: Caco2Expression_Caco2_withB_infantis_60mins_Rep2

value: ATTC HTB-37

value: Human colonic epithelial cells (Caco2)


title: Caco2Expression_Caco2Alone_30mins_Rep2

source_name: Caco2 expression at 30 mins incubation, time matched to infection assays


title: Caco2Expression_Caco2Alone_60mins_Rep1

value: 60 mins incubation, time matched to infection assays


title: Caco2Expression_Caco2Alone_30mins_Rep1

value: 30 mins incubation, time matched to infection assays


title: 211_RS_3

tag: tissue

tag: cell type

value: RENCA

value: day  2


title: 207_NR_1


title: melanoma_FFPE_12 [20170815_Karen02_K16_04]

source_name: primary melanoma FFPE tissue

tag: age at diagnosis

tag: tag


title: melanoma_FFPE_13 [20170815_Karen02_K17_05]

value: F

value: Absent


title: 204_NR_11


title: melanoma_FFPE_10 [20170815_Karen02_K14_02]

value: IIA

value: Alive


title: 205_NR_12


title: melanoma_FFPE_8 [20170815_Karen01_K12_12]

value: Present

value: primary cutaneous melanoma tissue


title: melanoma_FFPE_9 [20170815_Karen02_K13_01]

value: M

value: Sinai


title: melanoma_FFPE_6 [20170815_Karen01_K10_10]


title: melanoma_FFPE_7 [20170815_Karen01_K11_11]

value: IIC


title: h26844_78_lv

city: St. Louis

first: Mathieu

last: Garand

state: MO

address: One Childrens Place Suite 6120

department: Surgery

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were aligned to GRCh38 (GENCODE 20) with STAR version 2.0.4b
A count of a per million threshold equivalents to ∼10 raw expression value
Filtered transcripts were then annotated to gene symbols using org.Hs.eg.db and org.Mm.eg.db
Assembly: GRCh38
Supplementary files format and content: .csv; matrix of raw counts, transcripts (ENSG ID) as rows and samples as columns

source_name: Heart Tissue

extract_protocol:
MagneSil® PMPs on the Promega Maxwell 16
SMARTer Ultra Low RNA kit (Takara-Clontech)

value: Heart Tissue

tag: disease

value: No Disease

tag: group

value: LV

tag: Sex

value: female

tag: gestational age


title: h26844_78_rv

value: RV


title: h26834_89_rv


title: melanoma_FFPE_4 [20170815_Karen01_K08_08]

tag: cohort

tag: stage at original diagnosis

tag: ajcc thickness

tag: breslow thickness


title: melanoma_FFPE_15 [20170815_Karen02_K21_09]

tag: tnm

tag: ulceration

tag: os


title: 202_RS_1

tag: strain

value: BALB/c

value: Tumour

tag: timepoint


title: melanoma_FFPE_3 [20170815_Karen01_K05_05]

tag: gender

tag: pfs

tag: dead or alive at last contact


title: 059_NR_8

tag: tissue

tag: cell type

value: RENCA

value: day  0


title: melanoma_FFPE_2 [20170815_Karen01_K04_04]

value: F

tag: age at diagnosis

value: Dead

tag: tag


title: 203_RS_10

value: day  2


title: h26820_126_rv

tag: disease

value: HLHS

tag: group

tag: Sex

tag: gestational age


title: h26826_94_rv


title: h26826_94_lv


title: 058_NR_7